Linear ion traps are finding many applications in many areas of mass spectrometry. These applications typically demand facilitation of tandem mass spectrometry (MS/MS) techniques, measurement of high mass-to-charge (m/z) ratios, large dynamic range, precision, high quality data and throughput. This is particularly the case for biological or biochemical applications. In the proteomic field for example, where analytical instruments are required to identify both small and large molecules and to determine molecular structure, and required to do so quickly whilst providing high quality results. These instruments are required to identify thousands of peptides covering a large dynamic range from a single sample. Peptide identifications based on tandem mass spectrometry or MS/MS fragmentation of the peptides are also required. In addition, this particular field of technology typically dictates a high level of automation to accommodate a vast amount of data in minimal time. For these reasons new apparatus and methods which allow linear ion traps to respond to such demands are therefore sought.